.gitignore
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CLAUDE.md
LICENSE
MANIFEST.in
README.md
contributing.md
pyproject.toml
requirements.txt
setup.cfg
setup.py
.github/workflows/deploy_bioscrape.yml
.github/workflows/pypi_release.yml
.github/workflows/test_bioscrape.yml
Bioscrape.egg-info/PKG-INFO
Bioscrape.egg-info/SOURCES.txt
Bioscrape.egg-info/dependency_links.txt
Bioscrape.egg-info/not-zip-safe
Bioscrape.egg-info/requires.txt
Bioscrape.egg-info/scm_file_list.json
Bioscrape.egg-info/scm_version.json
Bioscrape.egg-info/top_level.txt
bioscrape/__init__.py
bioscrape/analysis.py
bioscrape/inference.cpp
bioscrape/inference.pxd
bioscrape/inference.pyx
bioscrape/inference_setup.py
bioscrape/pid_interfaces.py
bioscrape/random.cpp
bioscrape/random.pxd
bioscrape/random.pyx
bioscrape/sbmlutil.py
bioscrape/simulator.cpp
bioscrape/simulator.pxd
bioscrape/simulator.pyx
bioscrape/types.cpp
bioscrape/types.pxd
bioscrape/types.pyx
bioscrape/vector.pxd
docs/conf.py
docs/index.rst
docs/requirements.txt
docs/_static/custom.css
docs/api/core.rst
docs/api/index.rst
docs/api/inference.rst
docs/api/io.rst
docs/api/optional_lineage.rst
docs/developer/contributing.rst
docs/developer/index.rst
docs/examples/advanced-examples.nblink
docs/examples/basic-examples.nblink
docs/examples/benchmarking.nblink
docs/examples/birth-death-inference.nblink
docs/examples/fast-statistics.nblink
docs/examples/index.rst
docs/examples/inference-delay-models.nblink
docs/examples/inference-getting-started.nblink
docs/examples/interacting-lineages.nblink
docs/examples/lineage-examples.nblink
docs/examples/linear-model-inference.nblink
docs/examples/multi-trajectory-initial.nblink
docs/examples/multiple-measurements-inference.nblink
docs/examples/multiple-trajectories-inference.nblink
docs/examples/od-least-squares.nblink
docs/examples/priors-inference.nblink
docs/examples/sensitivity-analysis.nblink
docs/examples/stochastic-inference.nblink
docs/reference/paper.rst
docs/user_guide/bioscrape_xml.rst
docs/user_guide/delays.rst
docs/user_guide/examples.rst
docs/user_guide/installation.rst
docs/user_guide/lineage_package.rst
docs/user_guide/model_api.rst
docs/user_guide/overview.rst
docs/user_guide/parameter_inference.rst
docs/user_guide/propensities.rst
docs/user_guide/sbml_support.rst
docs/user_guide/sensitivity.rst
docs/user_guide/simulators.rst
examples/Advanced Examples and Developer Overview.ipynb
examples/Basic Examples - START HERE.ipynb
examples/Benchmarking bioscrape performance.ipynb
examples/Fast Statistics for SSA Trajectories.ipynb
examples/Sensitivity Analysis using Bioscrape.ipynb
examples/models/repressilator_sbml.xml
examples/models/sbml_test.xml
inference examples/Bioscrape Inference - Getting Started.ipynb
inference examples/Inference with Delay Models.ipynb
inference examples/OD data using least squares (LMFit example).ipynb
inference examples/birth_death_data_multiple_conditions.csv
inference examples/data/birth_death_data.csv
inference examples/data/birth_death_data_multiple_conditions.csv
inference examples/data/birth_death_data_multiple_param_conditions.csv
inference examples/data/data_toy_model.csv
inference examples/data/multiple_measurements.csv
inference examples/data/od_data.csv
inference examples/data/test_data.csv
inference examples/individual examples/Birth death model.ipynb
inference examples/individual examples/Linear Model.ipynb
inference examples/individual examples/Multiple measurements.ipynb
inference examples/individual examples/Multiple trajectories initial conditions.ipynb
inference examples/individual examples/Multiple trajectories.ipynb
inference examples/individual examples/Priors in Bioscrape Inference.ipynb
inference examples/individual examples/Stochastic Inference.ipynb
inference examples/individual examples/emcee_parallel.py
inference examples/individual examples/emcee_serial.py
inference examples/individual examples/multiple_measurements_corner.png
inference examples/individual examples/multiple_measurements_data_and_initial_sim.png
inference examples/individual examples/parallel_bioscrape_inference.py
inference examples/models/toy_sbml_model.xml
lineage/__init__.py
lineage/lineage.pxd
lineage/lineage.pyx
lineage examples/Interacting Lineages (Beta).ipynb
lineage examples/Lineage Examples.ipynb
lineage examples/ToggleCRN.xml
lineage tests/Event and Rule Testing.ipynb
lineage tests/GlobalCRNTwoCellTypeLineageTest.py
lineage tests/Interacting Lineage Tests.ipynb
lineage tests/Interacting Lineages via SBML.ipynb
lineage tests/SingleCellTypeTest.py
lineage tests/TwoCellTypeLineageTest.py
lineage tests/turbidostat_mode_timing.png
lineage tests/turbidostat_mode_timing.py
tests/How to write bioscrape tests.ipynb
tests/Likelihood and Data Objects.ipynb
tests/Saving and loading SBML and Bioscrape XML.ipynb
tests/dbg.txt
tests/debug_state.py
tests/test_inference.py
tests/test_initialize_model.py
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tests/test_propensities_via_annotations.py
tests/test_randomized_delay.py
tests/test_randomized_propensity.py
tests/test_rules.py
tests/test_sbml_loading.py
tests/test_sensitivity_analysis.py
tests/test_serialization.py
tests/test_simulator_statistics.py
tests/test_utils.py
tests/frozen_sbml_outputs/models/delay_model.xml
tests/frozen_sbml_outputs/models/hill_negative_crn.xml
tests/frozen_sbml_outputs/models/hill_negative_crn_bs.xml
tests/frozen_sbml_outputs/models/hill_positive_crn.xml
tests/frozen_sbml_outputs/models/hill_positive_crn_bs.xml
tests/frozen_sbml_outputs/models/massaction_1_crn.xml
tests/frozen_sbml_outputs/models/massaction_1_crn_bs.xml
tests/frozen_sbml_outputs/models/massaction_2_crn.xml
tests/frozen_sbml_outputs/models/massaction_2_crn_bs.xml
tests/frozen_sbml_outputs/models/prop_hill_negative_crn.xml
tests/frozen_sbml_outputs/models/prop_hill_negative_crn_bs.xml
tests/frozen_sbml_outputs/models/prop_hill_positive_crn.xml
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tests/frozen_sbml_outputs/random_propensities/general.xml
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tests/frozen_sbml_outputs/random_propensities/hillnegative.xml
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tests/frozen_sbml_outputs/random_propensities/hillpositive.xml
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tests/frozen_sbml_outputs/random_propensities/massaction.xml
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tests/frozen_sbml_outputs/random_propensities/proportionalhillnegative.xml
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tests/frozen_sbml_outputs/random_propensities/proportionalhillpositive.xml
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tests/frozen_sim_results/random_delays/fixed_stochastic.npy
tests/frozen_sim_results/random_delays/gamma_stochastic.npy
tests/frozen_sim_results/random_delays/gaussian_stochastic.npy
tests/frozen_sim_results/random_model_strings/ODEs.npy
tests/frozen_sim_results/random_model_strings/reactions.npy
tests/frozen_sim_results/random_propensities/general_deterministic.npy
tests/frozen_sim_results/random_propensities/general_stochastic.npy
tests/frozen_sim_results/random_propensities/hillnegative_deterministic.npy
tests/frozen_sim_results/random_propensities/hillnegative_stochastic.npy
tests/frozen_sim_results/random_propensities/hillpositive_deterministic.npy
tests/frozen_sim_results/random_propensities/hillpositive_stochastic.npy
tests/frozen_sim_results/random_propensities/massaction_deterministic.npy
tests/frozen_sim_results/random_propensities/massaction_stochastic.npy
tests/frozen_sim_results/random_propensities/proportionalhillnegative_deterministic.npy
tests/frozen_sim_results/random_propensities/proportionalhillnegative_stochastic.npy
tests/frozen_sim_results/random_propensities/proportionalhillpositive_deterministic.npy
tests/frozen_sim_results/random_propensities/proportionalhillpositive_stochastic.npy
tests/temp/birth_death_data_multiple_conditions.csv
tests/temp/birth_death_data_multiple_param_conditions.csv
tests/temp/serializable_model.xml
tests/temp/test_data.csv
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